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13 pages, 2347 KiB

Open AccessArticle

A Comparative Analysis of the Stomach, Gut, and Lung Microbiomes in Rattus norvegicus

by Taif Shah, Yuhan Wang, Yixuan Wang, Qian Li, Jiuxuan Zhou, Yutong Hou, Binghui Wang and Xueshan Xia

Microorganisms 2023, 11(9), 2359; https://doi.org/10.3390/microorganisms11092359 - 21 Sep 2023

Cited by 1 | Viewed by 1240

Abstract

Urban rats serve as reservoirs for several zoonotic pathogens that seriously endanger public health, destroy stored food, and damage infrastructure due to their close interaction with humans and domestic animals. Here, we characterize the core microbiomes of R. norvegicus’s stomach, gut, and lung [...] Read more.

Urban rats serve as reservoirs for several zoonotic pathogens that seriously endanger public health, destroy stored food, and damage infrastructure due to their close interaction with humans and domestic animals. Here, we characterize the core microbiomes of R. norvegicus’s stomach, gut, and lung using 16S rRNA next-generation Illumina HiSeq sequencing. The USEARCH software (v11) assigned the dataset to operational taxonomic units (OTUs). The alpha diversity index was calculated using QIIME1, while the beta diversity index was determined using the Bray–Curtis and Euclidean distances between groups. Principal component analyses visualized variation across samples based on the OTU information using the R package. Linear discriminant analysis, effect sizes (LEfSe), and phylogenetic investigation were used to identify differentially abundant taxa among groups. We reported an abundance of microbiota in the stomach, and they shared some of them with the gut and lung microbiota. A close look at the microbial family level reveals abundant Lactobacillaceae and Bifidobacteriaceae in the stomach, whereas Lactobacillaceae and Erysipelotrichaceae were more abundant in the gut; in contrast, Alcaligenaceae were abundant in the lungs. At the species level, some beneficial bacteria, particularly Lactobacillus reuteri and Lactobacillus johnsonii, and some potential pathogens, such as Bordetella hinzii, Streptococcus parauberis, Porphyromonas pogonae, Clostridium perfringens, etc., were identified in stomach, gut, and lung samples. Moreover, the alpha and beta diversity indexes revealed significant differences between the groups. Further analysis revealed abundant differential taxonomic biomarkers, i.e., increased Prevotellaceae and Clostridia in the lungs, whereas Campylobacteria and Lachnospirales were richest in the stomachs. In conclusion, we identified many beneficial, opportunistic, and highly pathogenic bacteria, confirming the importance of urban rats for public health. This study recommends a routine survey program to monitor rodent distribution and the pathogens they carry and transmit to humans and other domestic mammals. Full article

(This article belongs to the Special Issue Gut Microbiome in Homeostasis and Disease)

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17 pages, 3368 KiB

Open AccessArticle

Improvements in Gut Microbiome Composition Predict the Clinical Efficacy of a Novel Synbiotics Formula in Children with Mild to Moderate Atopic Dermatitis

by Chi Tung Choy, Pui Ling Kella Siu, Junwei Zhou, Chi Ho Wong, Yuk Wai Lee, Ho Wang Chan, Joseph Chi Ching Tsui, Claudia Jun Yi Lo, Steven King Fan Loo and Stephen Kwok Wing Tsui

Microorganisms 2023, 11(9), 2175; https://doi.org/10.3390/microorganisms11092175 - 28 Aug 2023

Cited by 1 | Viewed by 1426

Abstract

Atopic dermatitis (AD) is a common chronic inflammatory skin disease with a significant association with various type-2 inflammation-related comorbidities. Ongoing research suggests the crucial involvement of gut microbiome, especially in childhood onset AD, and hence, probiotics have emerged as a potential non-steroid-based therapeutics [...] Read more.

Atopic dermatitis (AD) is a common chronic inflammatory skin disease with a significant association with various type-2 inflammation-related comorbidities. Ongoing research suggests the crucial involvement of gut microbiome, especially in childhood onset AD, and hence, probiotics have emerged as a potential non-steroid-based therapeutics option to complement existing AD management plans. In order to delineate the impact of probiotics in the gut microbiome of pediatric AD patients from southern China, targeted 16S rRNA sequencing and thorough bioinformatic analysis were performed to analyze the gut microbiome profiles of 24 AD children after taking an orally administered novel synbiotics formula with triple prebiotics for 8 weeks. A notable improvement in Eczema Area and Severity Index (EASI) (p = 0.008) was observed after taking an 8-week course of probiotics, with no adverse effects observed. The relative abundances of key microbial drivers including Bacteroides fragilis and Lactobacillus acidophilus were significantly increased at week 8. We also found that the positive responsiveness towards an 8-week course of probiotics was associated with improvements in the gut microbiome profile with a higher relative abundance of probiotic species. Over-represented functional abundance pathways related to vitamin B synthesis and peptidoglycan recycling may imply the underlying mechanism. In summary, our study suggests how the gut microbial landscape shifts upon probiotic supplementation in AD children, and provides preliminary evidence to support targeted probiotic supplementation for the management of childhood AD. Full article

(This article belongs to the Special Issue Gut Microbiome in Homeostasis and Disease)

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14 pages, 4506 KiB

Open AccessArticle

Bibliometric Analysis of Global Trends in Research on Seasonal Variations in Gut Microbiota from 2012 to 2022

by Jiancheng Zhai, Xiao Sun, Rui Lu, Xueqin Hu and Zhiqiang Huang

Microorganisms 2023, 11(8), 2125; https://doi.org/10.3390/microorganisms11082125 - 21 Aug 2023

Viewed by 1018

Abstract

Seasons are the important influencing factor for gut microbiota, which in turn affects the ecology and evolution of the host. The seasonal variation in gut microbiota has increasingly attracted the attention of researchers and professionals worldwide. However, studies of seasonal variations in gut [...] Read more.

Seasons are the important influencing factor for gut microbiota, which in turn affects the ecology and evolution of the host. The seasonal variation in gut microbiota has increasingly attracted the attention of researchers and professionals worldwide. However, studies of seasonal variations in gut microbiota have not been systematically analyzed by bibliometrics or visual analysis. This study is based on 271 publications from 2012 to 2022 in the Web of Science Core Collection database (WOSCC) to analyze hot spots and trends in this field. The collaborations between different countries, institutions, authors, journals, and keywords were bibliometrically analyzed using Excel, CiteSpace (Version 6.2. R4), and VOSviewer (version 1.6.19) software. The number of publications has been increasing rapidly and shows a general upward trend. China and the Chinese Academy of Sciences are the country and institution contributing the most, respectively. The research hotspots and trends mainly include the diversity of gut microbiota communities in different seasons, the relationship between diet and gut microbiota in seasonal changes, and the relationship between gut microbiota and evolutionary adaptation in seasonal changes. This is the first bibliometric and visualization analysis of seasonal variations in gut microbiota, which may advance this field and lay the foundation for future research. Full article

(This article belongs to the Special Issue Gut Microbiome in Homeostasis and Disease)

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29 pages, 4275 KiB

Open AccessArticle

Could the Urease of the Gut Bacterium Proteus mirabilis Play a Role in the Altered Gut–Brain Talk Associated with Parkinson’s Disease?

by Matheus V. C. Grahl, Brenda da Silva Andrade, Ana Paula A. Perin, Gilda A. Neves, Laura de Souza Duarte, Augusto Frantz Uberti, Kelvin Siqueira Hohl, Cristian Follmer and Celia Regina Carlini

Microorganisms 2023, 11(8), 2042; https://doi.org/10.3390/microorganisms11082042 - 09 Aug 2023

Cited by 1 | Viewed by 1279

Abstract

Intestinal dysbiosis seems to play a role in neurodegenerative pathologies. Parkinson’s disease (PD) patients have an altered gut microbiota. Moreover, mice treated orally with the gut microbe Proteus mirabilis developed Parkinson’s-like symptoms. Here, the possible involvement of P. mirabilis urease (PMU) and its [...] Read more.

Intestinal dysbiosis seems to play a role in neurodegenerative pathologies. Parkinson’s disease (PD) patients have an altered gut microbiota. Moreover, mice treated orally with the gut microbe Proteus mirabilis developed Parkinson’s-like symptoms. Here, the possible involvement of P. mirabilis urease (PMU) and its B subunit (PmUreβ) in the pathogenesis of PD was assessed. Purified proteins were given to mice intraperitoneally (20 μg/animal/day) for one week. Behavioral tests were conducted, and brain homogenates of the treated animals were subjected to immunoassays. After treatment with PMU, the levels of TNF-α and IL-1β were measured in Caco2 cells and cellular permeability was assayed in Hek 293. The proteins were incubated in vitro with α-synuclein and examined via transmission electron microscopy. Our results showed that PMU treatment induced depressive-like behavior in mice. No motor deficits were observed. The brain homogenates had an increased content of caspase-9, while the levels of α-synuclein and tyrosine hydroxylase decreased. PMU increased the pro-inflammatory cytokines and altered the cellular permeability in cultured cells. The urease, but not the PmUreβ, altered the morphology of α-synuclein aggregates in vitro, forming fragmented aggregates. We concluded that PMU promotes pro-inflammatory effects in cultured cells. In vivo, PMU induces neuroinflammation and a depressive-like phenotype compatible with the first stages of PD development. Full article

(This article belongs to the Special Issue Gut Microbiome in Homeostasis and Disease)

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13 pages, 929 KiB

Open AccessArticle

Association between Helicobacter pylori Infection and Nasal Polyps: A Systematic Review and Meta-Analysis

by Michael Doulberis, Jannis Kountouras, Thomas Stadler, Christian Meerwein, Stergios A. Polyzos, Hasan Kulaksiz, Michael H. Chapman, Gerhard Rogler, Daniele Riva, Ioannis Linas, John Kavaliotis, Evangelos Kazakos, Maria Mouratidou, Christos Liatsos and Apostolis Papaefthymiou

Microorganisms 2023, 11(6), 1581; https://doi.org/10.3390/microorganisms11061581 - 14 Jun 2023

Cited by 4 | Viewed by 1934

Abstract

Background: Helicobacter pylori (H. pylori) has definite or possible associations with multiple local and distant manifestations. H. pylori has been isolated from multiple sites throughout the body, including the nose. Clinical non-randomized studies with H. pylori report discrepant data regarding the [...] Read more.

Background: Helicobacter pylori (H. pylori) has definite or possible associations with multiple local and distant manifestations. H. pylori has been isolated from multiple sites throughout the body, including the nose. Clinical non-randomized studies with H. pylori report discrepant data regarding the association between H. pylori infection and nasal polyps. The aim of this first systematic review and meta-analysis was the assessment of the strength of the association between H. pylori infection and incidence of nasal polyps. Methods: We performed an electronic search in the three major medical databases, namely PubMed, EMBASE and Cochrane, to extract and analyze data as per PRISMA guidelines. Results: Out of 57 articles, 12 studies were graded as good quality for analysis. Male-to-female ratio was 2:1, and age ranged between 17–78 years. The cumulative pooled rate of H. pylori infection in the nasal polyp group was 32.3% (controls 17.8%). The comparison between the two groups revealed a more significant incidence of H. pylori infection among the nasal polyp group (OR 4.12), though with high heterogeneity I² = 66%. Subgroup analysis demonstrated that in European studies, the prevalence of H. pylori infection among the nasal polyp group was significantly higher than in controls, yielding null heterogeneity. Subgroup analysis based on immunohistochemistry resulted in null heterogeneity with preserving a statistically significant difference in H. pylori infection prevalence between the groups. Conclusion: The present study revealed a positive association between H. pylori infection and nasal polyps. Full article

(This article belongs to the Special Issue Gut Microbiome in Homeostasis and Disease)

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15 pages, 2835 KiB

Open AccessArticle

Gut Microbiome and Associated Metabolites Following Bariatric Surgery and Comparison to Healthy Controls

by Adilah F. Ahmad, Jose A. Caparrós-Martín, Silvia Lee, Fergal O’Gara, Bu B. Yeap, Daniel J. Green, Mohammed Ballal, Natalie C. Ward and Girish Dwivedi

Microorganisms 2023, 11(5), 1126; https://doi.org/10.3390/microorganisms11051126 - 26 Apr 2023

Cited by 3 | Viewed by 1564

Abstract

The gut microbiome plays a significant role in regulating the host’s ability to store fat, which impacts the development of obesity. This observational cohort study recruited obese adult men and women scheduled to undergo sleeve gastrectomy and followed up with them 6 months [...] Read more.

The gut microbiome plays a significant role in regulating the host’s ability to store fat, which impacts the development of obesity. This observational cohort study recruited obese adult men and women scheduled to undergo sleeve gastrectomy and followed up with them 6 months post-surgery to analyse their microbial taxonomic profiles and associated metabolites in comparison to a healthy control group. There were no significant differences in the gut bacterial diversity between the bariatric patients at baseline and at follow-up or between the bariatric patients and the cohort of healthy controls. However, there were differential abundances in specific bacterial groups between the two cohorts. The bariatric patients were observed to have significant enrichment in Granulicatella at baseline and Streptococcus and Actinomyces at follow-up compared to the healthy controls. Several operational taxonomic units assigned to commensal Clostridia were significantly reduced in the stool of bariatric patients both at baseline and follow-up. When compared to a healthy cohort, the plasma levels of the short chain fatty acid acetate were significantly higher in the bariatric surgery group at baseline. This remained significant when adjusted for age and sex (p = 0.013). The levels of soluble CD14 and CD163 were significantly higher (p = 0.0432 and p = 0.0067, respectively) in the bariatric surgery patients compared to the healthy controls at baseline. The present study demonstrated that there are alterations in the abundance of certain bacterial groups in the gut microbiome of obese patients prior to bariatric surgery compared to healthy individuals, which persist post-sleeve gastrectomy. Full article

(This article belongs to the Special Issue Gut Microbiome in Homeostasis and Disease)

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Review

Jump to: Research

19 pages, 2033 KiB

Open AccessReview

Gut Microbiome–Colorectal Cancer Relationship

by Devvrat Yadav, Chiranjeevi Sainatham, Evgenii Filippov, Sai Gautham Kanagala, Syed Murtaza Ishaq and Thejus Jayakrishnan

Microorganisms 2024, 12(3), 484; https://doi.org/10.3390/microorganisms12030484 - 27 Feb 2024

Viewed by 1790

Abstract

Traditionally, the role of gut dysbiosis was thought to be limited to pathologies like Clostridioides difficile infection, but studies have shown its role in other intestinal and extraintestinal pathologies. Similarly, recent studies have surfaced showing the strong potential role of the gut microbiome [...] Read more.

Traditionally, the role of gut dysbiosis was thought to be limited to pathologies like Clostridioides difficile infection, but studies have shown its role in other intestinal and extraintestinal pathologies. Similarly, recent studies have surfaced showing the strong potential role of the gut microbiome in colorectal cancer, which was traditionally attributed mainly to sporadic or germline mutations. Given that it is the third most common cancer and the second most common cause of cancer-related mortality, 78 grants totaling more than USD 28 million have been granted to improve colon cancer management since 2019. Concerted efforts by several of these studies have identified specific bacterial consortia inducing a proinflammatory environment and promoting genotoxin production, causing the induction or progression of colorectal cancer. In addition, changes in the gut microbiome have also been shown to alter the response to cancer chemotherapy and immunotherapy, thus changing cancer prognosis. Certain bacteria have been identified as biomarkers to predict the efficacy of antineoplastic medications. Given these discoveries, efforts have been made to alter the gut microbiome to promote a favorable diversity to improve cancer progression and the response to therapy. In this review, we expand on the gut microbiome, its association with colorectal cancer, and antineoplastic medications. We also discuss the evolving paradigm of fecal microbiota transplantation in the context of colorectal cancer management. Full article

(This article belongs to the Special Issue Gut Microbiome in Homeostasis and Disease)

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42 pages, 4461 KiB

Open AccessReview

A Scoping Review Evaluating the Current State of Gut Microbiota Research in Africa

by Sara M. Pheeha, Jacques L. Tamuzi, Bettina Chale-Matsau, Samuel Manda and Peter S. Nyasulu

Microorganisms 2023, 11(8), 2118; https://doi.org/10.3390/microorganisms11082118 - 20 Aug 2023

Cited by 3 | Viewed by 1467

Abstract

The gut microbiota has emerged as a key human health and disease determinant. However, there is a significant knowledge gap regarding the composition, diversity, and function of the gut microbiota, specifically in the African population. This scoping review aims to examine the existing [...] Read more.

The gut microbiota has emerged as a key human health and disease determinant. However, there is a significant knowledge gap regarding the composition, diversity, and function of the gut microbiota, specifically in the African population. This scoping review aims to examine the existing literature on gut microbiota research conducted in Africa, providing an overview of the current knowledge and identifying research gaps. A comprehensive search strategy was employed to identify relevant studies. Databases including MEDLINE (PubMed), African Index Medicus (AIM), CINAHL (EBSCOhost), Science Citation index (Web of Science), Embase (Ovid), Scopus (Elsevier), WHO International Clinical Trials Registry Platform (ICTRP), and Google Scholar were searched for relevant articles. Studies investigating the gut microbiota in African populations of all age groups were included. The initial screening included a total of 2136 articles, of which 154 were included in this scoping review. The current scoping review revealed a limited number of studies investigating diseases of public health significance in relation to the gut microbiota. Among these studies, HIV (14.3%), colorectal cancer (5.2%), and diabetes mellitus (3.9%) received the most attention. The top five countries that contributed to gut microbiota research were South Africa (16.2%), Malawi (10.4%), Egypt (9.7%), Kenya (7.1%), and Nigeria (6.5%). The high number (n = 66) of studies that did not study any specific disease in relation to the gut microbiota remains a gap that needs to be filled. This scoping review brings attention to the prevalent utilization of observational study types (38.3%) in the studies analysed and emphasizes the importance of conducting more experimental studies. Furthermore, the findings reflect the need for more disease-focused, comprehensive, and population-specific gut microbiota studies across diverse African regions and ethnic groups to better understand the factors shaping gut microbiota composition and its implications for health and disease. Such knowledge has the potential to inform targeted interventions and personalized approaches for improving health outcomes in African populations. Full article

(This article belongs to the Special Issue Gut Microbiome in Homeostasis and Disease)

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